MetNetComp Database [1] / Minimal gene deletions Minimal gene deletions for simulation-based growth-coupled production. You can also see maximal gene deletions.

Model : iML1515 [2].
Target metabolite : udpg_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (80 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b2242 b3553 b3831 b3614 b0910 b3752 b2781 b1004 b3713 b1109 b0046 b1612 b1611 b4122 b1779 b1759 b2210 b1033 b2440 b1415 b4388 b4138 b4123 b0621 b4381 b2406 b3028 b1380 b3918 b1912 b2240 b1206 b0221 b2285 b3893 b1474   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.450203 (mmol/gDw/h)
  Minimum Production Rate : 0.056420 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.391504
  EX_o2_e : 287.043388
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.682030
  EX_pi_e : 0.547108
  EX_so4_e : 0.113370
  EX_k_e : 0.087877
  EX_mg2_e : 0.003906
  EX_ca2_e : 0.002343
  EX_cl_e : 0.002343
  EX_cu2_e : 0.000319
  EX_mn2_e : 0.000311
  EX_zn2_e : 0.000154
  EX_ni2_e : 0.000145
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992769
  EX_h2o_e : 551.559446
  EX_co2_e : 37.382990
  EX_succ_e : 0.469468
  EX_ura_e : 0.262841
  EX_etha_e : 0.181353
  Auxiliary production reaction : 0.056420
  DM_5drib_c : 0.000101
  DM_4crsol_c : 0.000100

Visualization
  1. Download JSON file.
  2. Go to Escher site [3].
  3. Select "Data > Load reaction data" and apply the downloaded file.

References
[1] Tamura, T. MetNetComp: Database for minimal and maximal gene deletion strategies for growth-coupled production of genome-scale metabolic networks, IEEE/ACM Transactions on Computational Biology and Bioinformatics, in press.
[2] Norsigian, C. J., Pusarla, N., McConn, J. L., Yurkovich, J. T., Dräger, A., Palsson, B. O., & King, Z. (2020). BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree. Nucleic acids research, 48(D1), D402-D406.
[3] King, Z. A., Dräger, A., Ebrahim, A., Sonnenschein, N., Lewis, N. E., & Palsson, B. O. (2015). Escher: a web application for building, sharing, and embedding data-rich visualizations of biological pathways. PLoS computational biology, 11(8), e1004321.

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Last updated: 21-Sep-2023
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